A genome sequence for the threatened whitebark pine

• Published in: G3 : genes - genomes - genetics 2024-05, Vol.14 (5)
• Main Authors: Neale, David B, Zimin, Aleksey V, Meltzer, Amy, Bhattarai, Akriti, Amee, Maurice, Figueroa Corona, Laura, Allen, Brian J, Puiu, Daniela, Wright, Jessica, De La Torre, Amanda R, McGuire, Patrick E, Timp, Winston, Salzberg, Steven L, Wegrzyn, Jill L
• Format: Article
• Language: English
• Subjects: Endangered Species; Genome Report; Genome, Plant; Genomics - methods; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Pinus - genetics; Pinus - parasitology
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1093/g3journal/jkae061

Abstract Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.Whitebark pine (Pinus albicaulis), a white pine of western North American subalpine regions, has become critically threatened throughout its range by white pine blister rust fungus (WPBR), mountain pine beetle, wildfire, and maladaptation from changing climate—vast acreages have suffered nearly complete mortality from WPBR. As genomic data can contribute to faster, cost-effective approaches for identifying disease-resistant, climate-adapted seed sources for restoration, Neale et al. present a high-quality reference sequence and annotation—a marked improvement in candidate WPBR-disease-resistance gene identification compared to previous assessments.